Master Chief Chronicles: The Search for Cortana
by jedihunter80
Summary: SPOILERS! FINALLY UPDATED AFTER MORE THAN A YEAR! After Halo 3, Master Chief is awakened on a planet outside of UNSC control. With Cortana in the hands of a strange man and with no one he knows to back him up, the next mission of John 117 begins!
1. He Moved

Jedihunter80: Hello, everybody! This is my first Halo Fanfic, and I hope you enjoy. Comment, please, but NO FLAMES! This first chapter is just a small teaser to get opinions on how the story will work. It picks up after the events of Halo 3. So, you could call this Halo 4 (the game we will NEVER see o0 )

SPOILERS 

This is the Spoiler alert system. This is not a test. This Fanfic contains spoilers for Halo 3, so please don't read if you do not want the ending spoiled. This has been the Spoiler Alert System.

SPOILERS 

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**Chapter 1: He Moved**

Ken Sanders was the director of the Museum of Science, City of Kajiim, planet of Celeron. It was a planet of humans that existed outside of the Milky Way galaxy, about 10 light-years from planet Onyx, never having made contact with the UNSC. They had advanced space travel, yes, just not that advanced. It was, however, advanced enough to pick-up a large metal object moving slowly towards Onyx in space, find it, and bring it back. And now Ken was proudly about to open the exhibit containing what was found inside that metal object. He stood at the head of a journalism crew; he was leading them on a private first-look tour of the exhibit to get publicity.

"Gentlemen," he rumbled in a deep baritone voice, "I welcome you to the first section of the exhibit: humans beyond our world." He gestured to a display case behind him that held six suits held up by mannequins: the battle uniforms of UNSC Marines. "We know they are human by remains found in various corridors on the derelict. They match our own skeletal structure exactly. We assume it was a military vessel because of the suits here…" he moved a little ways farther and gestured to another case "…and by the rifles here. If you can't tell already, their technology was quite a bit more advanced than ours…"

The tour continued passed photos, artists' depictions, bits and pieces of random things taken from the derelict's interior. On and on, many things lined the walls. Until they reached the end: a large, circular room with two objects in the center: a pedestal and an oblong object shrouded by a cloth. "…and it will remain in orbit until disassembled. Now, this…this is the crowning jewel of the exhibit. First: what we believe to be the ship's main memory unit." A computer chip sat in the middle of the pedestal, a glowing blue circle in the center. "Unfortunately, it appears to have burned out several years ago. And this," he turned to the cloth-shrouded object. "OPEN IT UP, BOYS!" The cloth fell. Cameras flashed. Jaws dropped.

"What is it?" one young reporter gaped.

"We think it is a coffin…and it has a completely preserved human inside. We want you to witness the opening of it so we can study him." Military Police had silently moved into position around the pod, rifles ready in case something was inside the "coffin". "Get your film ready, boys, this is history." He turned to some men behind a control desk. "On 3: 1…2…3!"

A loud beeping admitted from the pod as it was unsealed. Steam hissed. The canopy opened. The person inside could now be clearly seen. He was tall, clad entirely in a greenish-gold armor with a golden visor on the helmet. The armor was badly beaten and scratched, but the white "117" and Master Chief Petty Officer insignia where clearly shown on his chest. But the most surprising thing about him was not his looks, not the fact he was a human from a distant world, but the fact that he…moved.


	2. Escape

Jedihunter80: GAAHHHH

Jedihunter80: GAAHHHH! It's been over 3 months since my last update! I'm sorry, please don't hurt me…anyways, the point is that I'm back in action, and the next chapter of Master Chief Chronicles is here. I know it's a little short, but it should tide you over until chapter 3 comes later this week.

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**Chapter 2: Escape**

John was sitting in the middle of a green field, on a planet he distantly recognized. He was a young boy, dressed in a simple t-shirt that depicted a UNSC Marine battalion ready for battle; a propaganda shirt from the early days of the Covenant war. _I'm home. At least, I think this is home…it's been ages._ He stood and looked around. He was in a small suburban area, with nice houses built on a scenic overlook of a lake. It was sunset. _Was it all a dream…Dr. Hasely, the war, Cortana, all of it a dream? _

"John!" He turned, but saw nothing. _That voice, so familiar._ "John! It's getting late, time to come inside!" _My mother? Could it be?_

"John, don't go inside." _Now that voice I know._ He turned in the other direction, and found himself staring straight at…

"Cortana. When did you become…human?"

"I'm not. This is a dream John, but in this dream your decision of where to go decides your fate."

"Come again?"

"You have been in cryo for years. You are awakening, but your conscious is still weak. It's like the tunnel of light people see when they die…if you go that way, towards the light, towards your home, you will never awake from this dream. But, if you come back with me, things return to normal."

"And why would I not want to return home?"

"Because we still need you. I need you. And you said-"

"Wake me when you need me. Yeah, I remember." He took one last look at his home, his mother's voice fading away. _Goodbye again mother, I still love you…_

* * *

The museum security guards stepped back as the man in the "coffin" suddenly snapped to and almost leapt out of the pod. The reporters began to edge towards the exit.

"You said he was preserved, not alive!" shouted a younger man. Ken was startled as well, but quickly regained his composure and turned to the men at the control panel.

"Any life signs on that guy?"

"Yes, sir. His body appears to be fully functional, but he's in a dazed state. Give him a minute to adjust. There's no telling how long he's been in there." Ken turned back to the man, watching him slowly stand up and support himself on the pod he had emerged from.

"Just keep an eye on him. We could use this to our advantage." Ken approached the Master Chief, as he seemed to have fully returned to consciousness. "Greetings, friend. Do you speak basic?" The Chief stared back.

"I have no idea what that is, but your speaking my language. Now, where exactly am I?"

"A museum on the wonderful planet of Celeron, city of Kajim."

"Please, don't sugar coat it." The Chief took in his surroundings, looking at the old tattered uniforms and such that lined the walls. _Wait…what happened to…_"have you seen anybody else here? Particularly someone named Cortana."

"I'm afraid that you are the only survivor. I'm sorry, I can arrange a memorial service for all those lost on your ship if you'd like."

"I'd take it, but Cortana can't die like normal people."

"Say what?" Ken was doing his best to maintain an image of understanding, and the reporters were furiously scribbling on their notepads.

"Cortana is a computer AI…an intelligent hologram basically." _And yet, she seems like so much more…_The Chief shook himself out of it. He had to concentrate on finding Cortana and getting out of there. He felt around his equipment, trying to make it look as if he was running a diagnostics test, and checked for any remaining weapons. _One bubble shield, two plasma grenades, and a pistol. Not a great start, but I've been in worse situations. _He closely examined the layout of the museum. The ceiling was high, but between his genetic engineering and the added strength of the suit, he could make the jump with little effort. He could probably stick a grenade to the ceiling while Ken and his men were distracted (Ken was currently rambling about why Master Chief should stay at the building). _But where is Cortana?_ He surveyed the salvaged equipment lining the room until his eyes settled on the computer chip in the center. _Gotcha._ He slowly started edging closer, but Ken caught him as the Chief reached out his hand to pick her up.

"Ah, I'm afraid I cannot let you have that. It's museum property." Ken gave a quick signal to the men at the control desk, and instantly the pedestal on which Cortana's chip sat had disappeared into the ground. The Chief whipped out his pistol but suddenly found himself surrounded by Ken's security guards armed with heavier weapons. "Such rude behavior," Ken teased. "I just can't allow you to go out like this. Now, if you will please come this way to the lab-" but the Chief had already armed a grenade.

"I don't think so." People scattered as he threw the grenade into the air, and it stuck quickly to the ceiling. He just stood there as the blast went off, letting the debris bounce off his armor. "See you, boys." He jumped.

"STOP HIM!" Ken yelled to the nearest group of guards, and they took off to the roof access catch up. He then turned to the head of security and spoke quietly and quickly. "Listen up. I finally established complete control, and I will not have an incident like this stirring up more support for the UPA. It sounds crazy, but I know they will find a way to use it against us." He fell silent for a moment. "Scramble the special ops squads, I want him dead or alive." The security Chief nodded and the two walked off into the depths of the museum.

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Jedihunter80: Will the Chief get away? Who is the UPA? And who exactly is Ken and what is he in control of? All of this will be answered in the next exciting chapter, WHICH WILL COME THIS WEEK, I SWEAR!


	3. The Underworld

Jedihunter80: As you can tell, it's been quite a while since my last update *motions to the inch of dust on the ground* but the important thing is: I'm back! And since I've had forever to think about this story, I should be able to crank out a couple good chapters pretty quickly. I apologize to all of the loyal readers who have been sending me support for this story well after a year since the last update. I will not disappoint!

IMPORTANT NEW NOTE: I was cruising around some of the other stories on here and noticed they had some of the same story elements that I wanted to introduce later on. So if you see something that you recognize in upcoming chapters, know that I AM NOT TRYING TO STEAL FROM ANYONE! These are all ideas that I had when originally developing this story back in 2007/2008.

Thanks again for all of the support guys!!! And, with no further delay, on to the story!

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Chapter 3: The Underworld

The people of Celeron had never seen a SPARTAN in their lives, so Master Chief was bound to attract attention as he sprinted away from the museum. Realizing that he was turning almost every head that he passed, he ducked into an alley and hid behind a dumpster to catch his breath. _Such a short run shouldn't be wearing me out…I really was in that tube for a long time._ He needed to find a place where he could gather intel and strategize, and he needed to find it fast. Seeing a ladder to the roof of an apartment building, he quickly climbed to the top and began assessing his surroundings.

The city of Kajim was layed out in a standard grid pattern, much like those found on earth. In the center was a large, circular building with a huge spire extending from the center. It was surrounded by about two dozen skyscrapers, all of which were smaller than the spire on the center building. John guessed that this was the downtown business district. Outside of that were countless apartment buildings of varying sizes and styles, like the one he was standing on now. Turning around he saw the buildings shrink and thin out, eventually turning into nice suburban homes, and those in turn thinned out and abruptly ended in a very dry desert. He also noted that the civilians largely traveled in flying cars, and that the streets were only used by foot traffic and the occasional car or delivery van. Turning back to the view of downtown, Master Chief observed a rather large group of armored troop carriers, air vehicles, and foot soldiers leaving the museum in a search pattern, doubtlessly coming for him. He jumped from the top of the building back into the alley and headed for the closest cover he could find: a manhole cover.

Dropping down into the sewer, John soon found himself ankle deep in sludge. He reached back up and replaced the manhole cover, doing his best to make it look undisturbed. He wandered around for a minute before coming to a large opening on the side of the sewer where he could sit down. _I have two options,_ he began to think, _#1: Try to eliminate the troops coming after me and try to take Cortana back by force, starting a one-man war. #2: ditch my armor _he shuddered at this thought _and blend in with the population. Gain more intel and get Cortana back when the opportunity presents itself._ He didn't like it one bit, but with no intel, no backup, no Cortana, and because he was still experiencing the after-effects of a long cryo freeze, John was going to have to go stealth and just wait this one out. The man walked along the wall, tapping the bricks until he found a large hollow spot. Using his combat knife to cut out the aging mortar, he removed several bricks and began to strip down. By the time he was done, John was dressed in nothing but a black, skin-tight t-shirt and black combat pants and boots that he kept stored in the back compartment of his suit. He placed everything else in the small cave that he made, keeping only the pistol, remaining plasma grenade, and a small PDA he could use to take notes and make a map of the city. Carefully replacing the bricks in the wall, John marked the coordinates on his PDA so he could find the location later. Then, looking back one last time and feeling rather naked, Master Chief began walking in a direction away from the museum.

* * *

Ken Sanders sat down in the big chair behind his desk, in his office located at the top of the tall spire. On either side of his desk stood heavily armed guards, who he immediately dismissed as a man in a white lab coat entered.

"Your honor," the man bowed, "I have the item you requested."

"Cut the formalities, Stephen. You've been my friend since the revolution. I'm not going to cut your head off for being casual with me"

Stephen smiled. "Well now that you hold the title of Emperor, I didn't know if you still wanted to associate with me or not."

Ken laughed, " I didn't name you the head of my research and development division for nothing, you know. But down to business. There was some kind of computer chip in that case, and the man from the coffin wanted it. Think you can get in there and find out what it is?"

Now it was Stephen's turn to laugh. "Please, Ken, I'm the one who hacked the entire military network for you during the takeover. This will be simple. In fact we can get to work on it right now, if you will follow me to the lab."

"Let's get to it," said Ken, a sinister grin spreading across his usually calm face. The two men left the office together, laughing evilly as they went.

* * *

John must have been walking for at least two hours in the sewer before he finally came upon a dead end. Cautiously he climbed to the manhole cover and slowly opened it, just enough so that he could see outside. Seeing no one, he removed the cover completely and emerged into the outskirts of town. This was someplace he hadn't seen in his brief survey of the area; it appeared to be an abandoned railroad yard. Everywhere there were rows upon rows of abandoned train cars…all full of makeshift beds and campfires. He had stumbled upon a very large hobo camp.

"Hey, Mick," someone called from behind him, "we have a newbie here." John turned around to see three men walking towards him.

"Well howdy stranger," spoke the man in the middle of the three, "what brings you to our humble camp?" Calling on years of training, John spun a fake story on the fly.

"Lost my job last week, got kicked out of my house shortly after that. I've got nothing left, and I am in need of a place to spend the night." The man known as Mick studied him for a minute, his wise old eyes staring into John's very soul, and finally answered with a warm smile.

"There has been a lot of that going around since the democracy fell in the bloody revolution. This new dictatorship of Sander's is ruining the economy and putting a lot of people on the streets. Just look around you, this is what we call 'The Underworld'," he motioned to the sea of ragged men sitting around campfires. John stiffened at the mention of Ken's name. _Dictatorship UNDER Ken…this changes everything._ Mick continued, "I'll get you a bed and some basic provisions that will last a few days. You can pick up more daily rations after that at our 'Headquarters', which is in that abandoned building over yonder. Welcome to your new home, friend." The three men began to walk away, but Mick stopped one more time. "By the way, what is your name?"

"John," he paused, "John Spartan"

* * *

Jedihunter80: ah, the plot thickens! Not a lot of action in this one, but I hope it will tide you over until tomorrow or Tuesday, when you can expect chapter 4. More twists and answers can be expected!!!


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